New York — Paul Mankiewicz, a biologist, botanist, and erstwhile philosopher, has a vision for New York City. He calls it “zero discharge”: Not a drop of water should escape from the city without first making something grow.

Rainwater should be caught and used to cultivate greenery. “Gray water” from showers, baths, and sinks should irrigate rooftop gardens. Trees dotting streets are good, but a belt of grasses and shrubs lining roadways would better catch and utilize runoff. Restored wetlands around the city would filter any water that escapes. All water entering the city should pass through a natural system on its way out.

“What you have to do is bring the land to life,” he says. “Our footprint is not an abode for life. It’s the opposite; it’s sterile.”

Mr. Mankiewicz, executive director of the Gaia Institute in New York and treasurer of the city’s Soil and Water Conservation District, has designed ecosystems for 30 years. He had a hand in the city’s very first “green streets,” patches of greenery sprouting up alongside roadways in recent years, and the Bronx’s first green roof.

Now he’s working with the city on a pilot project to restore oysters and mussels, keystone species, to city waterways. His guiding principle: Living systems can achieve naturally what humans endeavor to do artificially. Dirt can hold water and sequester heavy metals. Soil microbes and plant roots – “the symbiosis that runs the terrestrial biosphere,” he says – can digest the carbon-based molecules that collect in the average city gutter.

“You have to rethink the permeable and impermeable,” he says.

Beneath every square meter of soil run 15 to 20 miles of fine plant roots and perhaps 10,000 miles of filament-like fungal roots. Between 10 million and 10 billion microbes inhabit each cubic centimeter of soil. The right kind could decompose motor oil and gasoline, which are common in urban runoff. A cubic centimeter of humus, the fine, dark grains in soil, contains 2,000 square meters of surface area that binds to toxic heavy metals, like mercury.

Standing beside a 300-square-foot Bronx green street he helped design, Mankiewicz expounds on the value of living soil. Normally, the city has to treat runoff before releasing it into waterways. But this patch of green could absorb much of the 50,000 gallons of runoff generated here yearly. (Soil sensors will measure just how much.) Multiply that by some 2,000 green streets now in existence, and the result is some 100 million gallons of water not going down storm grates.

Over the years, Man­kie­wicz has em­­phasized the critical role of simple dirt, says Robert Alpern, an adviser in the city’s Department of Environmental Protection under former mayor David Dinkins: “His major contribution has been to sensitize everybody in the bureaucracies to the potential of soils as a filtration and infiltration medium for storm water.”

On St. Simon Stock Elementary School’s rooftop garden (finished in 2005), Mankiewicz explains the greatest hurdle to greening the city’s 35 square miles of rooftops: The average cubic foot of dirt weighs between 100 and 120 pounds, around three times the load for which most roofs are engineered.

So he designed his own soil, substituting ground polystyrene (Styrofoam) for much heavier sand and clay. The result, patented as GaiaSoil, weighs 10 pounds per cubic foot and can hold twice its weight in water. The next problem: New York gets about 40 inches of rain yearly, but it doesn’t come evenly. A recent dry spell has left some of the Little Blue Stems, one of perhaps 25 native species atop St. Simon’s roof, looking forlorn.

He notes the nearby boy’s bathroom. City dwellers pay $2 per 100 cubic feet of water, and $3 to treat it. Why not save $3? Gray water from the sink could be fed to the garden via solar-powered pump. He has to convince the city it’s safe first. “I want it so that people can build green roofs without the Department of Health worrying about it,” he says.

Mankiewicz grew up Bloomfield, N.J. When he was young, Bloomfield farmers grew vegetables to sell in New York City. He himself sold tomatoes from his mother’s garden door-to-door. But urban sprawl eventually did away with the fields. “All the areas I grew up with that were beautiful were paved over,” he says.

James Parks Morton, sometimes called “the green dean,” presided over and encouraged the religious-environmentalist ferment for 25 years, ending in 1997. He recalls one project in particular: Inside a bay of the soaring gothic cathedral, by some accounts the world’s largest, Mankiewicz constructed a living model of the Hudson River ecosystem: several 20-foot-long tanks filled with fish, “various green stuff,” and blue crabs.

“It was incredible, people saying, ‘My God, in a church?’ ” recalls Mr. Morton. “That was the point, to say that [the environment] is a deeply important, religious concern.”

In the 1980s, Mankiewicz itched to apply his ideas on ecosystem design to the real world. “People were saying, ‘interesting idea,’ but no one was doing anything,” he says. So in 1995, he incorporated the Gaia Institute, a nonprofit. “Nothing was going to change, otherwise,” he says.

It was an unusual move, says Dominick Basile, Mankiewicz’s PhD adviser at Lehman College in the Bronx. Most biologists choose the reliable paycheck of research or academia. But Mankiewicz and his wife, Julie – both of whom Dr. Basile describes as “brilliant” and “dedicated” – chose to “spread the gospel” of biology. “I really worried about them,” he says. “They’ve made some considerable material sacrifices.”

Says Mankiewicz: “If you want quick money, never get into the green-roof business.” For 25 years, the overriding problem was lack of interest from on high. City officials favored a hard engineering approach – chemicals and machinery – to solve issues like storm water runoff. Now that’s changing. “People are just [now] getting it,” he says.

The city now has 2,300 green streets, a program begun under mayor Rudolph Giuliani in the 1990s. Mayor Michael Bloomberg has pledged to surpass 3,000 by 2017. MillionTreesNYC aims to plant1 million more trees throughout the city in coming years. (The current tree census: 592,130.) It’s all inching the city closer to Mankiewicz’s “zero discharge” dream. “It would change the local climate,” he says, “and that would be magnificent.”